R: Write a Partition File for Clust&See

linkcomm2clustnsee {linkcomm} | R Documentation

## Write a Partition File for Clust&See

### Description

This function writes out a partition file which can be imported into the Cytoscape plug-in Clust&See.

### Usage

    linkcomm2clustnsee(x, file = "temp.cns", network.name = NULL)

### Arguments

`x` | An object of class `linkcomm` or `OCG`.
`file` | A character string naming a Clust&See partition file (.cns extension). Defaults to `"temp.cns"`.
`network.name` | A character string providing a name for the network. This name must correspond to the file name of the network that will be imported into Cytoscape. If NULL, the object name, `x`, is used. Defaults to NULL.

### Details

Cytoscape is an open source platform for complex-network analysis and visualization, and Clust&See (Spinelli et al. 2013) is a Cytoscape plug-in used for visualizing and manipulating the clusters produced by various network clustering algorithms.

### Value

Used for its side-effect of writing a Clust&See partition file to disk.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Becker, E. et al. (2012) Multifunctional proteins revealed by overlapping clustering in protein interaction network. Bioinformatics 28, 84-90.

Gambette, P. and Guenoche, A. (2011) Bootstrap clustering for graph partitioning. RAIRO-Operations Research 45, 339-352.

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

Shannon, P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504.

Spinelli, L. et al. (2013) Clust&See: a Cytoscape plugin for the identification, visualization, and manipulation of network clusters. BioSystems 113, 91-95.

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Write a partition file to disk.
    ## Not run:
    linkcomm2clustnsee(lc)

    ## End(Not run)

[Package linkcomm version 1.0-14 Index]